Example Jinja template for yaml config files

process.py

from jinja2 import Environment, PackageLoader, select_autoescape

def process(**kwargs):

  # set up Jinja env
  env = Environment(
          loader=PackageLoader(''),
          autoescape=select_autoescape(['html', 'xml'])
  )

  for i,t in enumerate(tsv_inputs):
    # render the template contents as a string into the var contents
    contents = env.get_template('test_config.yaml.j2').render(
            tsv_input = t,
            **kwargs
    )
    # write to a file (or do whatever else)
    with open('test_config_%d.yaml'%(i+1),'w') as f:
      f.write(contents)

      
if __name__=="__main__":
  process(bananas="this is bananas")

test_config.yaml.j2

# nema: a non-random subset of data from Tulin et al. (2013), that can
# be used to do assembly and comparative expression analysis.

# this sets the output directory name:
basename: 'nema'

# this describes the samples:
samples: "{{ tsv_input }}"

{{ bananas }}

# this says to download samples specified as Web URLs:
get_data:
  download_data: True